Computational Genomics

Overview: 

The main focus of our group is to decipher and understand the biology of genomes. Genomes, as the molecule of life, contain the necessary information for the development and evolution of living organisms. Despite this information is encoded in a four-letter code; it presents different levels of complexity. The comparison of genomic and derived sequences allows us to uncover the general rules and patterns that control and make life possible. Our research activity uses computational and experimental approaches to reach these goals by finding answers to specific molecular, evolutionary and biomedical questions.

 

RESEARCH DIRECTOR
ICREA
Torrents Arenales, David (ICREA Research Professor)

Objectives: 

genomics torrentsCurrently, we have different research lines open:

- Identification and characterization of gene regulatory regions. Our goal is to understand how these regions evolve, and whether there are regular patterns and particular conservation levels depending on the nature and function of groups of eukaryotic genes, particularly within vertebrates. For this, we are first developing and then applying different computational tools to identify promoter regions and enhancers. Our approaches combine the use of sequence conservation at different levels: directly from alignments, through the mapping and evaluation of transcription factor binding boxes and, in collaboration with the group of Modesto Orozco of our department, also exploring the potential of the conservation of DNA structural properties in the prediction and characterization of these regulatory regions. All these analysis are also combined with experimental validation carried out within our group.  

-Analysis of regulatory regions in metagenomic data. Our goal is to determine and explore how the organisms associated to different environments control their gene expression. Our approach is based on the application of different prediction software and existing databases to identify promoter regions in bacteria and then compare them. As with the analysis of proteins, this study can highlight new pathways and strategies that might have an impact in ecology, evolution and biomedicine. Our group has a permanent collaborative activity with the group of Peer Bork (EMBL) for the analysis of metagenomic data at different levels. 
-Systems biology of complex diseases. In the context of a Collaborative Project supported by European Commission (MITIN, Grant Agreement no. HEALTHF4-2008-223450; http://mitin-fp7.eu/), we are developing the necessary methodology and tools to generate a computational framework for the study of complex diseases. In particular, we have started a pilot phase by modeling the insulin signaling pathway and the biology of the mitochondria, as well as the cross-talk between these two biological systems to analyze its implication in Diabetes and Obesity. On top of these research lines, our group is actively collaborating with a number of groups around the world by providing our expertise and tools. The unique computational environment where we are located, make us able to reach levels of comparison and analysis that allow answering more complex biological questions.

PEOPLE

PUBLICATIONS AND COMMUNICATIONS

2012

González, S., et al. ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. Bioinformatics (2012).at <http://bioinformatics.oxfordjournals.org/content/28/6/763.long>
Adams, D., et al. BLUEPRINT to decode the epigenetic signature written in blood. Nature biotechnology 30, 224-6 (2012).

2011

Rossi, D., et al. Identification of a potent and selective σ₁ receptor agonist potentiating NGF-induced neurite outgrowth in PC12 cells. Bioorganic & medicinal chemistry 19, 6210-24 (2011).
Fernandez, M., Caballero, J., Fernandez, L. & Sarai, A. Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM). Molecular diversity 15, 269-89 (2011).
Arumugam, M., et al. Enterotypes of the human gut microbiome. Nature 473, 174-80 (2011).
Puente, X.S., et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101-5 (2011).

2010

Fernandez, M., Caballero, J., Fernandez, L. & et al., Graphical Representations of Protein Sequences for Alignment-Free Comparative and Predictive Studies. Recognition of Protease Inhibition Pattern from H-Depleted Molecular Graph Representat. Bioinformatics (2010).
Ballana, E., et al. ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 50, 1022-32 (2010).
Fernández-Real, J.M., et al. Transferrin receptor-1 gene polymorphisms are associated with type 2 diabetes. European journal of clinical investigation 40, 600-7 (2010).

2008

Quijano, C., et al. Selective maintenance of Drosophila tandemly-arranged duplicated genes. (2008).

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